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This transmission electron microscope image shows SARS-CoV-2—also known as 2019-nCoV, the virus that causes COVID-19. isolated from a patient in the U.S., emerging from the surface of cells cultured in the lab.

Source: NIAID-RML

Even as the number of global Covid-19 infections drops across the world, leading U.S. health officials are warning of a coming wave of infections as new, more contagious — and possibly more deadly — variants of the virus take hold in the U.S.

Scientists aren’t surprised by the emergence of the new variants and have reiterated that the currently available vaccines should still work against them — albeit, a bit less effective than as against the original, “wild” strain. However, top U.S. health officials and infectious disease experts worry that these highly contagious variants, particularly the B.1.1.7 strain that emerged in the U.K., could reverse the current downward trajectory in infections in the U.S. and delay the country’s recovery from the pandemic.

“I think we should be assuming that the next wave of case growth, to the extent that we have it, is going to be with B.1.1.7, and that’s something that I think everybody has to be even more cautious about,” Andy Slavitt, White House Covid-19 senior advisor, told MSNBC last week. “It’s nice to see the numbers of cases drop, but it could be misleading.” 

Why viruses mutate

As the coronavirus spreads, it makes huge numbers of copies of itself, and each version is a little different from the one before it, experts say. SARS-CoV-2, the virus that causes Covid-19, has had plenty of opportunities to spread and replicate. As more people become infected, the more likely it is that problematic mutations will arise.

The three main “variants of concern” that have U.S. officials on edge were first identified in the United Kingdom, South Africa and Brazil. The B.1.1.7 variant, first found in the U.K., is rapidly multiplying in the United States and is likely to become the nation’s dominant strain by March, according to a January study by the U.S. Centers for Disease Control and Prevention.

Through mutating, the virus is simply trying to “get to the next host and make more of itself,” Dr. Adam Lauring, an infectious diseases expert at the University of Michigan in Ann Arbor, told the JAMA network in a Feb. 4 interview. Like other coronaviruses, SARS-CoV-2 tends to mutate more slowly than other viruses such as the flu because it has a “proofreading” enzyme that fixes some of the changes when it replicates.

In other cases, “escape mutations” allow the virus to adapt to “selective pressure,” which is when the virus encounters a population that already has some degree of immunity against it — whether through prior infection, vaccination or antibody treatments — that limits its ability to spread but doesn’t stop it.

“You can think of it as trying out new solutions,” Lauring said. “Either that mutation is going to make you a better virus or a worse virus, and then what you have is selection. Survival of the fittest, for the lack of a better term.”

Research shows that more worrisome virus mutations could be coming from people who are immunocompromised, since it takes their bodies longer to respond and clear the virus, giving it more time to figure us out and mutate, said Dr. Dennis Burton, the Scripps Research Institute chair of immunology and microbiology.

“If somebody has the virus, and they clear it in a couple of days, you’ve not got much chance to mutate,” Burton told CNBC in a phone interview. “But if somebody has the virus, like an immunocompromised person, and they harbor the virus for weeks, then it’s going to have a lot more chance to mutate.”

Why some are worse than others

Only a small number of variants become a public health concern, infectious diseases experts say. Those variants typically become easier to spread, cause more severe illness in people who are infected, or evade some of the protections from vaccines and antibodies.

CDC Director Dr. Rochelle Walensky told JAMA on Wednesday that the B.1.1.7 variant is thought to be roughly 50% more transmissible and early data indicates it could be up to 50% more virulent, or deadly.

There’s also evidence to suggest that people infected with earlier strains of the virus could be reinfected with the B.1.351 variant, found in South Africa, Walensky wrote in a JAMA viewpoint with White House Chief Medical Advisor Dr. Anthony Fauci and Dr. Henry Walke, the CDC’s Covid incident manager.

SARS-CoV-2 is a coronavirus, which is a large family of viruses named “for the crown-like spikes on their surfaces,” according to the CDC. Researchers monitor those spikes, or the S-protein, for mutations because they can allow the virus to bind to cells easier or increase the amount of virus a person sheds.

The S-protein has what’s called a “receptor binding domain” that acts like “the hand of the spike” that grabs hold of what’s known as an ACE2 receptor on human cells, Dr. Daniel Griffin, chief of infectious diseases for ProHEALTH, told CNBC.

Changes to the S-protein could be a problem because those spikes have been the target of neutralizing antibodies that fight Covid-19 and are created through natural infection or vaccination, Griffin said. They could also impact the performance of monoclonal antibody therapies that prevent people from developing severe illness.

For instance, the B.1.1.7 variant first identified in the U.K. has several different mutations, according to the CDC. One of the key mutations, N501Y, is a change in the spike protein that scientists think helps the virus bind to cells easier.

The same key N501Y mutation has separately developed in the B.1.351 variant, identified in South Africa, and the P.1 variant, found in Brazil. Both strains have also developed another concerning mutation in their spike proteins, known as E484K.

The CDC warns that this mutation, which has now been identified in some B.1.1.7 cases, could be resistant to antibody drug therapies, and early studies show that it may reduce the effectiveness of some vaccines.

“This is the one that actually gets me concerned,” Griffin told CNBC, referring to the E484K mutation.

What this means for vaccines

While the vaccines have still proven to be effective against the variants, there’s concern that the B.1.351 strain could present some challenges.

Large clinical trials from Johnson & Johnson and Novavax reported in late January that their vaccines dipped in effectiveness when tested in South Africa. Novavax said its vaccine was just 49% effective among 44 Covid-19 cases in South Africa, and J&J said its vaccine was 57% effective at preventing symptomatic Covid-19.

The World Health Organization’s immunization director, Kate O’Brien, said on Thursday that these results don’t provide much certainty because the number of cases in the South African trials were low.

“We’re in still these early days of interpreting the evidence and, again, the most important thing is to get more information about what’s actually happening with respect to disease,” O’Brien said at a press briefing. “In general, we see that the vaccines retain efficacy against disease albeit at a lower level in settings without the variants that are highly prevalent.”

Pfizer and Moderna

Clinical trials from PfizerBioNTech and Moderna were performed before the variants emerged, so scientists have been performing laboratory tests to determine how well blood samples from people who were already vaccinated react to lab-constructed virus variants with the key mutations.

Those studies, which look at whether the sera in the blood neutralizes the virus and prevents it from replicating, have shown a reduction in performance when tested against the B.1.351 variant. That “suggest(s) that currently employed vaccines might be less effective at preventing infection due to this variant,” Walensky, Fauci and Walke wrote in their viewpoint.

However, your body’s ability to fight off the virus might depend on more than just neutralizing antibodies, including T cells and B cells, which could help fight the virus but aren’t measured in the early lab assessments, Lauring told JAMA.

The good news is that the Pfizer and Moderna vaccines also showed a high efficacy rate in earlier trials — roughly 95%. So there’s a cushion that would allow for a dip in their performance while they would still be considered effective by doctors, experts say. The shots have also been shown to provide protection against people contracting severe forms of disease that would result in hospitalizations or death.

Both Pfizer and Moderna have already said they’re working on a booster shot for their vaccines that will hold up better against the B.1.351 strain.

Finding the mutations

The B.1.1.7 variant was first identified in the United Kingdom in December, but it’s thought to have emerged at some point in September. Many experts have credited the U.K.’s ability to conduct genomic sequencing on a wide scale for the discovery of the variant.

Genomic sequencing is a laboratory technique that breaks down the virus’s genetic code, allowing researchers to monitor how it changes over time and understand how these changes might affect it, according to the CDC.

In the U.S., there are now 1,661 documented Covid-19 cases with the B.1.1.7 variant, 22 cases with the B.1.351 variant and five cases with the P.1 variant, according to the CDC’s latest data. Officials acknowledge that the U.S. is sequencing a small fraction of cases and the spread of the variants is likely far broader. The federal government, however, has recently tried to ramp up how many samples it sequences each week to detect these variants and other mutations that may be developing domestically.

The CDC has partnered with public health and commercial laboratories to rapidly scale up the nation’s genomic sequencing. Walensky told JAMA on Wednesday that in January, the U.S. was sequencing only 250 samples per week, which has since grown “to the thousands.” She added that “we’re not where we need to be.”

Dr. Ilhem Messaoudi, the director of the University of California at Irvine’s Center for Virus Research, said the process can be time consuming and labor intensive but emerging strains will be missed if laboratories aren’t sequencing a certain percentage of all positive Covid-19 test results to find the new mutations.

“Now we’re trying to catch up,” she said in a phone interview with CNBC. “We’re like, ‘Let’s go back and see if we have this.'”

Masks and social distancing

The rapidly spreading variants renew the importance of suppressing the coronavirus’s spread through public health measures, such as wearing masks, socially distancing and practicing hand hygiene, to prevent further mutations and buy time for countries to deploy life-saving vaccines.

But coronavirus variants aren’t just a problem for the United States. If the virus circulates in other parts of the world that are unvaccinated, it could lead to mutations that may threaten the widely deployed vaccines in other countries, the head of the CDC warned on Wednesday.

Eventually, the whole world will need to build an immunity to the virus or else the variants will continue to be a problem, Burton told CNBC.

“Sooner or later variants will get everywhere if they’ve got a big advantage,” Burton said. “It’s a global problem; it’s not just a problem for any one country.”

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U.S. coronavirus relief package, currency moves, oil

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Vehicles are reflected in a window as electronic boards display stock information at the Australian Securities Exchange, operated by ASX.

Lisa Maree | Bloomberg | Getty Images

SINGAPORE — Asia-Pacific markets were set to trade higher Monday as investors reacted to last week’s U.S. jobs report that trounced expectations and fueled hopes for a faster economic recovery.

Australian shares opened in the green. The benchmark ASX 200 climbed 1.73% in early trade as all sectors traded higher, with the heavily-weighted financials subindex adding 1.83%. Major banking and mining stocks rose: Shares of Commonwealth Bank jumped 1.86% while Rio Tinto added 2.54%, Fortescue was up by 2.49% and BHP gained 2.57%.

Nikkei futures pointed to opening gains in Japan.

Monday’s session in Asia-Pacific is set to follow a wild day in U.S. markets last Friday, where stocks roared back from a sharp sell-off as a stronger-than-expected nonfarm payrolls report improved optimism for a quicker economic recovery.

“Investors remain wary of the impact that the massive Biden fiscal experiment will have on longer-term interest rates, making for a fragile equity environment,” analysts at ANZ Research said in a morning note on Monday. “That defensiveness may prevail into the mid-March (Federal Open Market Committee) meeting.”

U.S. relief package

The U.S. Senate passed a $1.9 trillion coronavirus relief package over the weekend that includes direct payments of up to $1,400 to most Americans. The bill is expected to pass in the Democratic-held House this week and sent to President Joe Biden for his signature before a March 14 deadline to renew unemployment aid programs.

Last month, Fed Chair Jerome Powell told lawmakers that the U.S. economy was a long way from its employment and inflation goals and that it will likely take time for substantial further progress to be achieved. He said that inflation is still “soft” and that the Fed was committed to current policy, which implied interest rates are likely to remain low for now.

Currencies and oil

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Stock futures jump after Senate passes $1.9 trillion Covid relief bill, Dow futures up 200 points

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Traders work on the floor of the New York Stock Exchange.

NYSE

U.S. stock futures jumped on Sunday evening as a new stimulus package from Washington headed toward final passage this week.

Futures contracts tied to the Dow Jones Industrial Average jumped 219 points, or 0.7%. Those for the S&P 500 and the Nasdaq 100 composite gained 0.5% and 0.6%, respectively.

The move in futures came after the Senate passed a $1.9 trillion economic relief and stimulus bill on Saturday, paving the way for extensions to unemployment benefits, another round of stimulus checks and aid to state and local governments. The Democrat-controlled House is expected to pass the bill later this week. President Joe Biden is expected to sign it into law before unemployment aid programs expire on March 14.

The fresh round of government spending could cause ripples in the U.S. Treasury market, where the benchmark 10-year yield has risen sharply in recent weeks. The yield rose as high as 1.62% on Friday after starting the calendar year below the 1% mark.

The rapid move in the bond marked has unnerved equity investors as well, contributing to weakness in stocks with high valuations.

Futures contracts tied to the 10-year fell 0.2% on Sunday night at the open of trading, implying higher yields.

“10-year yields finally caught up to other asset markets. This is putting pressure on valuations, especially for the most expensive stocks that had reached nosebleed valuations,” Mike Wilson, the chief U.S. equity strategist at Morgan Stanley, said in a note.

The stock market is coming off an afternoon rally on Friday that took some of the sting out of a rough week for high-flying momentum names. The tech-heavy Nasdaq finished with a week-to-date loss of 2.1%, while the S&P 500 gained 0.8%. The Dow, more reliant on cyclical stocks, rose 1.8%.

The Friday turnaround doesn’t signal that the recent weakness for the market is over, but the divergence between tech and cyclical plays shows that the bullish story remains intact, Morgan Stanley’s Wilson said.

“The bull market continues to be under the hood, with value and cyclicals leading the way. Growth stocks can rejoin the party once the valuation correction and repositioning is finished,” Wilson said.

On the economic front, investors will get a look at wholesale inventory data from January on Monday. Several economic measures in recent weeks have shown a recovery that is picking up steam, including a better-than-expected February jobs report released on Friday.

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U.S. will defend troops after rocket attack in Iraq, Lloyd Austin says

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U.S. Defense Secretary Lloyd Austin speaks to Defense Department personnel during a visit by U.S. President Joe Biden at the Pentagon in Arlington, Virginia, February 10, 2021.

Carlos Barria | Reuters

WASHINGTON – Secretary of Defense Lloyd Austin warned those responsible for carrying out last week’s rocket attack against an Iraqi base that hosts American troops will be held to account.

“The message to those that would carry out such an attack is that expect us to do what is necessary to defend ourselves,” Austin said in an interview with ABC that aired on Sunday.

“We’ll strike if that’s what we think we need to do at a time and place of our own choosing. We demand the right to protect our troops,” he said, adding that the U.S. is still assessing intelligence with its Iraqi partners.

Defense officials have previously said the attack had typical hallmarks of a strike by Iran-backed groups. Iran has denied involvement.

When asked if Iran would view a potential U.S. response as an escalation of tensions, the new Pentagon chief and retired Army four-star reiterated that Washington would do whatever is necessary to protect Americans and U.S. interests in the region.

“What they [Iranians] should draw from this, again, is that we’re going to defend our troops and our response will be thoughtful. It will be appropriate,” Austin said. “We would hope that they would choose to do the right things,” he added.

On Sunday, the U.S. military’s Central Command, which oversees the wars in the Middle East, flew its fourth bomber deployment to the region.

The show of force mission included two B-52H Stratofortress bombers alongside aircraft from Israel, Saudi Arabia, and Qatar at different points to “deter aggression and reassure partners and allies of the U.S. military’s commitment to security in the region.”

Last month, Iran rejected an invitation from global powers who signed the 2015 nuclear deal to discuss the regime’s potential return to the negotiating table, a significant setback in the Biden administration’s efforts to revive the Joint Comprehensive Plan of Action, or JCPOA.

The White House said that the Biden administration was disappointed with Iran’s decision to skip the informal meeting but would “reengage in meaningful diplomacy to achieve a mutual return to compliance with JCPOA commitments.”

President of Iran, Hassan Rouhani speaks during the National Combat Board Meeting with Coronavirus (Covid-19) in Tehran, Iran on Nov. 21, 2020.

Iranian Presidency Handout | Anadolu Agency | Getty Images

The Biden administration has previously said that it wants to revive the nuclear deal but won’t suspend sanctions until Tehran comes back into compliance. Tehran has refused to negotiate while U.S. sanctions remain in place.

The 2015 JCPOA, brokered by the Obama administration, lifted sanctions on Iran that had crippled its economy and cut its oil exports roughly in half. In exchange for billions of dollars in sanctions relief, Iran agreed to dismantle some of its nuclear program and open its facilities to more extensive international inspections.

The U.S. and its European allies believe Iran has ambitions to develop a nuclear bomb. Tehran has denied that allegation.

In 2018, then-President Donald Trump kept a campaign promise and withdrew the United States from the JCPOA calling it the “worst deal ever.” Following Washington’s exit from the landmark nuclear deal, other signatories of the pact ⁠have tried to keep the agreement alive. 

Washington’s tense relationship with Tehran took several turns for the worse under the Trump administration.

President Donald Trump speaks during a briefing on Hurricane Michael in the Oval Office of the White House in Washington, DC, October 10, 2018. 

Saul Loeb | AFP | Getty Images

People gather to protest the US air strike in Iraq that killed Iranian commander Qasem Soleimani, who headed Iran’s Revolutionary Guards’ elite Quds force in Sanaa, Yemen on January 6, 2020.

Mohammed Hamoud | Andalou Agency | Getty Images

Soleimani’s death led the regime to further scale back compliance with the international nuclear pact. In January 2020, Iran said it would no longer limit its uranium enrichment capacity or nuclear research.

In October, the United States unilaterally re-imposed U.N. sanctions on Tehran through a snapback process, which other U.N. Security Council members have previously said Washington does not have the authority to execute because it withdrew from the nuclear deal in 2018.

A month later, a top Iranian nuclear scientist was assassinated near Tehran, which led Iran’s government to allege that Israel was behind the attack with U.S. backing.

A view shows the scene of the attack that killed Prominent Iranian scientist Mohsen Fakhrizadeh, outside Tehran, Iran, November 27, 2020.

WANA via Reuters

During the summer of 2019, a string of attacks in the Persian Gulf set the U.S. and Iran on a path toward greater confrontation.

In June 2019, U.S. officials said an Iranian surface-to-air missile shot down an American military surveillance drone over the Strait of Hormuz. Iran said the aircraft was over its territory. That strike came a week after the U.S. blamed Iran for attacks on two oil tankers in the Persian Gulf region and after four tankers were attacked in May.

The U.S. that June slapped new sanctions on Iranian military leaders blamed for shooting down the drone. The measures also aimed to block financial resources for Iran’s Supreme Leader Ayatollah Khamenei.

Tensions soared again in September of 2019 when the U.S. blamed Iran for strikes in Saudi Arabia on the world’s largest crude processing plant and oil field. The strikes forced the kingdom to shut down half of its production operations.

The event triggered the largest spike in crude prices in decades and renewed concerns of a budding conflict in the Middle East.

The Pentagon described the strikes on the Saudi Arabian oil facilities as “sophisticated” and represented a “dramatic escalation” in tensions within the region.

All the while, Iran maintains that it was not behind the attacks.

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